The goal of this research project is to develop a physical map of the mouse Y chromosome. Specifically, through our proposed research we will: 1) create a collection of 200 sequence tagged sites (STSs) distributed throughout the euchromatic portion of the mouse Y chromosome, 2) use the STSs to characterize a collection of deletion-hearing Y chromosomes, and 3) use the STSs to create an ordered array of yeast and/or bacterial artificial chromosome (YAC or BAC) clones spanning the euchromatic portion of the Y chromosome. Y-specific material isolated by bivariate fluorescence activated chromosome sorting, and/or subtractive hybridization of male and female genomic DNA, will be used to create an STS source library of small insert size (500 base pairs). Three to four hundred Y-specific clones will be sequenced with the goal of generating at least 200 single copy, Y- specific, STS primer pairs. The STSs win then be used to characterize a series of deletion-bearing Y chromosomes, giving order to both the STSs and the deletion breakpoints, and thereby creating a physical map of the Y. The STSs will also be used to isolate and order a contiguous series of YAC or BAC clones spanning the Y chromosome. Together, the proposed experiments will give us a deeper understanding of the structure and evolution of the Y chromosome. Moreover, by providing a direct molecular entry point for cloning genes borne on the Y, the proposed experiments will afford new insights into the study of sex determination, male fertility, and illnesses (such as hypertension and gonadoblastoma) that show an association with certain Y-linked alleles.